The adlayer structure of 1-octadecanethiol (1-C18H37SH) is investigated by scanning tunnelling microscopy (STM) with bare and chemically (I and S) modified Pt/Ir tips. The molecules were observed to form a well-ordered self-assembly monolayer on highly oriented pyrolytic graphite. The alkyl chains of molecules were clearly imaged by bare tips. The S-modified tip was found to be effective to reveal the structural details of thiol groups (SH). Based on the STM results and theoretical calculations, a model for a 1-octadecanethiol adlayer is proposed. Copyright (C) 2001 John Wiley & Sons, Ltd.